David De Roure

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A Web 2.0 Virtual Research Environment

• David De Roure
• University of Southampton, UK
• Carole Goble
• The University of Manchester, UK

OGF Semantic Grid Research Group www.semanticgrid
.org
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Overview

• Motivation
• Design
• Realisation

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E. Science laboris

• Workflows are the new rock and roll.
• Machinery for coordinating the execution of
  (scientific) services and linking together
  (scientific) resources.
• The era of Service Oriented Applications
• Repetitive and mundane boring stuff made easier.
• The challenge for biology is complexity and
  heterogeneity, not so much compute.

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Taverna Workflow Workbench
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Taverna domains

• Systems biology
• Proteomics
• Gene/protein annotation
• Microarray data analysis
• Medical image analysis
• Heart simulations
• High throughput screening
• Phenotypical studies
• Phylogeny
• Text mining
• Plants, Mouse, Human
• Astronomy

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Recycling, Reuse, Repurposing

• Paul meets Jo.
• Trypanosomiasis cattle workflow reused without
  change.
• Identified the biological pathways involved in
  sex dependence in the mouse model, previously
  believed to be involved in the ability of mice to
  expel the parasite.
• Previously a manual two year study, by Jo, of
  candidate genes had failed to do this.

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e-Services in the CLOUD

• Independent third party world-wide service
  providers of applications, tools and data sets.
  In the Cloud.
• 850 databases, 166 web servers Nucleic Acids
  Research Jan 2006
• My local applications, tools and datasets. In the
  Enterprise. In the laboratory.
• Easily incorporate new service without coding. So
  even more services from the cloud and enterprise.

• 3500 service operations
• All major providers
• Integration application for service providers
  like BioMOBY and BioMART

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e-Scientists in the CLOUD

• Individual life scientists, in under-resourced
  labs, who use other peoples applications, with
  little systems support.
• Exploratory workflows
• Developers (often) the users.
• Consumers are providers.

• A distributed, disconnected community of
  scientists.
• Decoupled suppliers and consumers of services and
  workflows.
• Scientists in an enterprise and in large projects
• Scientists out of the enterprise, in small
  projects or sole traders.

200 projects and sites, 1000 individual
users. Users throughout UK, USA, Europe, and SE
Asia
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39,326 total sourceforge downloads (4 October
2007). Ranked in sourceforge top 200 (June 07).
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Scientific memes. Scientific virusesAccompany
their published outcomes400 Scufl workflows in
the Web Cloud
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myExperiment.org Portal Party

• 28th 29th Sept 2006
• Hand picked Taverna users Taverna development
  team
• Facilitated by NCeSS.
• AJAX based development
• CombeChem xfer

• A social networking environment for sharing any
  workflow
• A Taverna workflow run environment
• A multi-workflow launch environment

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New Scientist
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openwetware.org
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Key evaluator and inspiration

• Cat De Roure
• Her idea.
• 15 years old.
• This is one of her MySpace pictures.
• Immediately understood it.
• Immediately could use it.
• Its like MySpace for science homework.

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myExperiment.org is

• A market place.
• A community social network.
• A gateway to other publishing environments.
• A federated repository
• A platform for launching workflows.
• Publishing self-describing encapsulated
  myExperiment Objects.
• Mindful publication.
• Started March 2007.

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myExperiment.org principles

• Make it easy to publish, easy to participate,
  easy to add value to though mash-ups
• Use familiar techniques
• Shopping, Social networking, gaming
• Use off the shelf, open source web tooling, not
  restrictive portals. Keep it funky, keep it
  flexible, keep it extensible. Assume other people
  will add functionality.
• Ruby on Rails, Facebook platform
• Aim it at young people. Make it fun and
  attractive. Say no to 1970s library interfaces!

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Scoping exercise

• Workflow warehouse / federation of repositories
  Open Archives Initiative. Federated
  myExperiments. Sharepoint.
• Social space organised rich site Social
  discourse organised service / workflow space
  using curated semantics.
• Granularity and identifiers Rolling-up
  provenance. Id resolution
• Open vs protected content Quality, Reliability,
  Validation, Safety, Intellectual Property,
  Ownership, Secrecy, A duty of guardianship.
  Curation? Policing? Local data mixed with shared
  resources
• Desktop integration Google gadgets for workflows.
  Interacting with workflows through Office
  products.
• Workflow execution (WHIP) Workflows Hosted in
  Portals project
• Evolving the myExperiment software Community
  development
• Enabling Scientists added value through
  applications and collaborative tagging

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Front End.A market place.A community social
network.User Participation.
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A Market Place Shoe Shop?

• Shopping for Workflows and Services and Data
  should be as easy as shopping for shoes.
• Dont need to train people.
• Fuel for diagnostics. Find a similar workflow.
• Organic growth good and bad.
• We need good, organised metadata for automated
  use.
• Impedance mismatch
• Identity and Ontology Authority

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Screen shot of bio Service shopping site
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A Social Network and Collective Intelligence

• Source of large amount of metadata.
• Open tagging, folksonomies, blogging, profiles,
  recommendations.
• Social network analysis and e-tracking are
  valuable intelligence.
• How do we avoid being deafened by the shouting?
• What are the incentive models for scientists?

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Semantic Sweatshop

• Service vocabularies and curation in the wild
• Keywords and tagging only goes some of the way.
• Curation
• Workflow metadata
• Find a workflow that is similar to what I want or
  need similar to this one. Or hers. Hmmmm.
• Recommendations, people profiles
• Fuel for discovery and diagnostics
• Pipeline from tag cloud to shop

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Leveraging and Serving The Long Tail of Users in
the Cloud

• Small labs or individuals
• Specialist workflows, Niche
• Expert and inexpert

• Big labs big groups
• Common de facto workflows

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Back End.Federated repositories.A gateway to
other publishing environments.A platform for
launching workflows.User Participation.
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Warehouse or Federation

• Community web site, federated repository.
• Multiple and My.
• Publish what I want when I want within the group
  I want.
• Mixed identity regimes an identity authority
• Open Archives Initiative. http//www.openarchives.
  org/
• The CombeChem project. http//www.combechem.org/

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A gateway to other publishing services

• Tryps team already has a wiki
• Mash up with Facebook and workflow hosting apps.
• Bring functionality to the user. Cooperate! Dont
  Control.

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We Need You! Cooperate, Don't Control

• A network of cooperating data services with
  simple interfaces which make it easy to work with
  content.
• Provides services
• Reuses the service of others.
• Support lightweight programming models so that it
  can easily be part of loosely coupled systems.
• You add a mashup!
• Workflows as content syndication?

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A platform popular request!

• See a workflow? Launch it! Coming soon.
• The ability to execute workflows from
  myExperiment integration of tools such as
  Taverna achieves increased value through usage
  network effects.
• And lets do that with Kepler, Triana etc
• The WHIPs project for a workflow hosting portal
  environment. Funded by OMII-UK. Run by Triana!
• Handling of results? Wiki pages?
• Workflows available through a variety of
  interfaces supporting workflow execution.

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Web 2.0 Design Patterns

• The Long Tail
• Data is the Next Intel Inside
• Users Add Value
• Network Effects by Default
• Some Rights Reserved
• The Perpetual Beta
• Cooperate, Don't Control
• Software Above the Level of a Single Device

• http//www.oreillynet.com/pub/a/oreilly/tim/news/2
  005/09/30/what-is-web-20.html

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1. The Long Tail

• Our target users are not just the specialist
  e-Scientists using computing resources to tackle
  major scientific breakthroughs, but also the
  large number of scientists conducting the routine
  processes of science on a daily basis.
• Through sharing we have the potential to enable
  smart scientists to be smarter and propagate
  their smartness, in turn enabling other
  scientists to become better and conduct better
  science.

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2. Data is the Next Intel Inside

• myExperiment understands that scientists are
  focused on data, not software or one particular
  workflow engine.
• Workflows are components of customised
  applications, many of which are data-oriented
  rather than process-oriented.
• Users manipulate, through their own applications,
  the product (data, model) yielded by the
  workflow.
• Furthermore, workflows themselves are the data of
  myExperiment and provide its unique value.

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3. Users Add Value

• myExperiment makes it easy to find workflows and
  is designed to make it useful and straightforward
  to share workflows and add workflows to the pool.
  
• To succeed we draw on the insights into the
  incentive models of scientists gained through
  experience with Taverna.

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4. Network Effects by Default

• myExperiment aggregates user data as a
  side-effect of using the VRE.
• The ability to execute workflows from
  myExperiment, and the integration of tools such
  as Taverna with myExperiment, further enable us
  to achieve increased value through usage.

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5. Some Rights Reserved

• myExperiment users require protection as well as
  sharing, but the environment is designed for
  maximum ease of sharing to achieve collective
  benefits workflows are "hackable" and
  "remixable".
• Initiatives such as Science Commons provide a
  useful context for this.

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6. The Perpetual Beta

• myExperiment is an online service (a collection
  of online services) and is continually evolving
  in response to its users.
• To support this, the project commenced with
  developers being embedded in the user community.
• Through day-to-day contact between designers and
  researchers, design is both inspired and
  validated.

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7. Cooperate, Don't Control

• myExperiment is a network of cooperating data
  services with simple interfaces which make it
  easy to work with content.
• It both provides services and reuses the service
  of others.
• It aims to support lightweight programming models
  so that it can easily be part of loosely coupled
  systems.

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8. Software Above the Level of a Single Device

• The current model of Taverna running on the
  scientists desktop PC or laptop is evolving into
  myExperiment being available through a variety of
  interfaces and supporting workflow execution.

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• myExperiment makes it really easy for the next
  generation of scientists to contribute to a pool
  of scientific workflows, build communities and
  form relationships
• It enables scientists to share, re-use and
  repurpose workflows and reduce time-to-experiment
  , share expertise and avoid reinvention
• myexperiment.org

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Hack Fest
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Web 2 Implementation
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Timeline

• Closed Beta released in July 2007
• Open Beta from November 2007
• In friends and family trials now with
  bioinformaticians and chemists
• Linking up to Triana
• Enactment and EMOs coming next
• Music and social science in pipeline

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Take homes

• myExperiment is a Web 2.0 Environment for
  Scientists to share experiments
• Join us!
• David De Roure
• dder_at_ecs.soton.ac.uk
• Carole Goble
• carole.goble_at_manchester.ac.uk

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Credits

• myGrid and CombeChem
• Matt Lee
• David Withers
• Don Cruickshank
• David Newman
• Mark Borkum
• Rob Procter
• Alex Voss
• Duncan Hull
• Katy Wolstencroft

• June Finch
• Ed Zaluska
• Jeremy Frey
• Simon Coles
• Danius Michaelides
• Paul Fisher
• Marco Roos
• Stian Soiland
• All the users inc. embedders